With the rise of the Internet, competitiveness is pressuring enterprises to build better solutions with fewer resources, following new trends and supporting new platforms and methodologies. On the other hand, legislation and regulations are updating frequently and deeply, and demanding rapid compliance from enterprises. These frequent business changes shake all the interoperability links between the enterprises, leading to periods of adaptation where business operation is not possible. The urge to rapidly regain interoperability often leads to unfounded, poorly-chosen solutions, which lead to inefficiency and rework. This paper proposes that the best way to have a strong interoperable environment is to perform constant, periodic maintenance operations in order to adapt enterprises to their surrounding ecosystem. It introduces NEGOSEIO, a framework that promotes continuous improvement and adaptation towards the management of interoperability on enterprise systems, and which has negotiations as a core mechanism to handle inconsistencies and solutions for the detected interoperability problems. Following this approach, enterprises shall become more adaptable to changes and external factors, consequently developing resilient and efficient interactions with its supply chain. The paper validates the framework with its application in a real business case of aerospace mission design on the European Space Agency (ESA).